Cotranslational folding in ab initio protein structure prediction and applications in de novo design;

PROTACs(蛋白水解靶向嵌合体)是一种异质双功能分子。它们通过与感兴趣蛋白(POI)和E3连接酶结合来发挥作用。使POI与E3连接酶紧密相连会导致多泛素化，这标志着POI被蛋白质小体降解。这种作用机制使PROTAC分子成为需要长期下调特定蛋白质[1][2]的治疗候选药物。许多PROTAC分子是从具有已知蛋白质结合特性的小分子中衍生出来的。一种常见的方法是将一个已知的小分子E3连接酶结合到另一个已知的小分子上，该小分子通过连接区(通常是聚乙二醇或聚乙二醇)结合目标蛋白质。该项目将涉及一种被称为IMID(免疫调节亚胺药物)的较小类型的分子。这类药物包括沙利度胺、来那度胺和泊马度胺。尽管在结构上与更传统的嵌合PROTAC分子不相似，但现在已知IMID通过类似PROTAC的机制展示其药效。该分子的酰亚胺成分--作为生物分子尿苷的类似物--在一个三色氨酸疏水口袋中与E3连接酶蛋白Cereblon结合。邻苯二甲酰亚胺分子的一半，从brablon E3连接酶蛋白中突出出来，改变了ereblon E3连接酶蛋白的表面拓扑结构图1 PROTACS作用机制：在没有protac分子的情况下，目标蛋白不会被降解；在protac存在的情况下，目标蛋白连接到E3连接酶，E3连接酶通过多泛素化标记它进行降解[13]，这样它现在就会与各种其他蛋白质结合，这些蛋白质都通过上述途径被标记为降解。尽管这些蛋白质的整体形状各不相同，但它们都有一个与IMID/Cereblon复合体结合的小基序。这个基序在初级序列方面不保守，但在每种情况下结构相似。还有一个保守的甘氨酸残基，它适应了IMID的邻苯二甲酰亚胺基序的结合。GSK进行的测试表明，这种共有的基序，以下称为降解基序，可以添加到蛋白质中，并在IMID药物存在的情况下用作降解的标签。这种方法被称为IPID(IMID邻近诱导降解)。对具有可变GlySer连接子长度的重组GFP-degron杂交物的分析证明了概念的正确性。GSK目前的一个研究目标是探索将这种开关包括在CAR-T细胞治疗(嵌合抗原受体T细胞治疗)中的可能性，这是一种免疫治疗形式，T细胞被修饰以识别和摧毁患者自己的癌细胞。实现这一点的蛋白质由融合到跨膜区的单抗的scFv区域组成。

PROTACs (proteolysis-targeting chimera) are heterobifunctional molecules. They function by binding to a protein of interest (POI) and an E3 ligase. Bringing the POI into close proximity with the E3 ligase leads to polyubiquitination, which marks the POI for degradation by the proteosome. This mechanism of action makes PROTAC molecules exciting candidates for therapies which require long-term downregulation of a specific protein [1] [2].Many PROTAC molecules are derived from small molecules with known protein binding properties. A frequent approach is to tether a known small molecule E3 ligase binder to a different small molecule that is known to bind the protein of interest via a linker region (usually polyethylene glycol, or PEG).This project will be concerned with a smaller class of molecules known as IMIDs (immunomodulatory imide drugs). Members of this drug class include thalidomide, lenalidomide, and pomalidomide. Although not structurally similar to the more traditional chimeric PROTAC molecules, it is now known that IMIDs exhibit their pharmaceutical effects via a PROTAC-like mechanism. The imide component of the molecule - acting as an analogue of the biomolecule uridine - binds to the E3 ligase protein cereblon in a triple tryptophan hydrophobic pocket. The phthalimide half of the molecule, protruding out from the cereblon E3 ligase protein, alters the surface topology of cereblonFigure 1 PROTACS mechanism of action: In the absence of the protac molecule, the target protein is not degraded; in the presence of the protac, the target protein is linked to an E3 ligase, which marks it for degradation via polyubiquitination [13]such that it will now bind with a variety of other proteins, which all become marked for degradation via the aforementioned route.Work by GSK has explored the conserved features found amongst these target proteins in nature. Although diverse in overall shape, these proteins all share a small motif which binds to the IMID/cereblon complex. This motif is not conserved in terms of primary sequence, but is structurally analogous in each case. There is also a conserved glycine residue, which accommodates binding of the phthalimde motif of the IMID. Any residue other than glycine in this position would be too sterically crowded.Tests carried out by GSK have shown that this shared motif, hereafter referred to as a degron, can be added to a protein and used as a tag for degradation in the presence of an IMID drug. This approach has been named IPID (IMID Proximity Induced Degradation). Assays involving recombinant GFP-degron hybrids with variable GlySer linker lengths demonstrate the proof of concept.A current research goal at GSK is to explore the possibility of including this switch in CAR-T cell therapy (chimeric antigen receptor T cell therapy), a form of immunotherapy where T cells are modified to recognise and destroy the patient's own cancer cells. The protein through which this is achieved comprises of the scFv region of a monoclonal antibody, fused to a transmembrane domain